4EB1: Antithrombin-III

Hyperstable in-frame insertion variant of antithrombin. Determined by X-ray diffraction at 2.8 Å resolution. Released 18 Jul 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,205
Mol. weight: 100.32 kDa
Ligands: NAG
Released: 18 Jul 2012

Explore 4EB1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EB1 contains 33 α-helices and 42 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain I: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	1
α-helix	25-26	2
α-helix	46-68	23
β-strand	76-78	3	2
α-helix	80-90	11
α-helix	91-93	3
α-helix	96-105	10
α-helix	108-110	3
β-strand	115	1	1
α-helix	116-127	12
α-helix	128-132	5
β-strand	138-149	12	3
β-strand	154	1	4
α-helix	156-166	11
β-strand	169-173	5	3
α-helix	179-193	15
β-strand	204-214	11	3
β-strand	219-232	14	3
β-strand	233	1	5
α-helix	236-238	3
α-helix	239-241	3
β-strand	243-248	6	2
β-strand	254-270	17	2
α-helix	272-274	3
β-strand	276-281	6	2
β-strand	282	1	5
β-strand	287-293	7	2
α-helix	300-306	7
α-helix	309-317	9
β-strand	320-329	10	2
β-strand	332-338	7	3
α-helix	340-345	6
α-helix	350-352	3
α-helix	360-362	3
β-strand	363	1	4
β-strand	370-382	13	3
β-strand	384	1	3
β-strand	387-388	2	3
β-strand	396-398	3	6
β-strand	408-411	4	2
β-strand	416-422	7	2
β-strand	427-434	8	2

Chain L: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	45-68	24
β-strand	76-78	3	6
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	116-118	3
α-helix	119-131	13
β-strand	139-149	11	7
β-strand	154	1	8
α-helix	156-165	10
β-strand	169-173	5	7
α-helix	179-193	15
β-strand	213-224	12	7
β-strand	225	1	9
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-240	6	6
β-strand	246-262	17	6
α-helix	264-266	3
β-strand	268-273	6	6
β-strand	274	1	9
β-strand	279-285	7	6
α-helix	292-296	5
α-helix	301-310	10
β-strand	312-322	11	6
β-strand	323-330	8	7
α-helix	332-337	6
α-helix	342-344	3
β-strand	355	1	8
β-strand	364-375	12	7
β-strand	379-390	12	7
β-strand	408-414	7	6
β-strand	419-426	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	I	protein	440	Homo sapiens	P01008 (AlphaFold model)
Antithrombin-III	L	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>4EB1_1 Antithrombin-III (chains I)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINVLVLVNTRTSTVLVLVNTIYFKGLWKSKFSPE
NTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSL
AKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLP
GIVAEGRDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFI
REVPLNTIIFMGRVANPCVK

Sequence of entity 2 (L), FASTA

>4EB1_2 Antithrombin-III (chains L)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance. Martinez-Martinez, I., Johnson, D.J., Yamasaki, M. et al. J Thromb Haemost (2012) 10:1859-1866. DOI 10.1111/j.1538-7836.2012.04839.x · PubMed

Other PDB entries of the same protein (UniProt P01008 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KCG 1.7 Å, Crystal structure of the antithrombin-factor IXa-pentasaccharide complex
2B5T 2.1 Å, 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic…
1TB6 2.5 Å, 2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex
1E04 2.6 Å, Plasma beta antithrombin-III
1JVQ 2.6 Å, Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive…
1NQ9 2.6 Å, Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State
2ANT 2.6 Å, The 2.6 a structure of antithrombin indicates a conformational change at the heparin…
1E05 2.62 Å, Plasma alpha antithrombin-III
1OYH 2.62 Å, Crystal Structure of P13 Alanine Variant of Antithrombin
1R1L 2.7 Å, Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an…
2BEH 2.7 Å, Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent…
1T1F 2.75 Å, Crystal Structure of Native Antithrombin in its Monomeric Form

Browse structure collections

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